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Genome wide screen

Eui Jae Sung, Stephen B Shears
OBJECTIVE: Invertebrates are productive models for understanding how inflammation, metabolism and aging are intertwined. We have deployed a dsRNA library screen to search for genes in Drosophila melanogaster-and hence identify human orthologs-that encode participants in a G-protein coupled, Ca2+ -signaling pathway that regulates inflammation, metabolism and lifespan. RESULTS: We analyzed receptor-dependent, phospholipase C/Ca2+ signaling responses to the growth-blocking peptide (GBP) cytokine in Drosophila S3 cells plated in 384-well plates containing dsRNAs that target approximately 14,000 Drosophila genes...
December 13, 2018: BMC Research Notes
Benoît Tessoulin, Agnès Moreau-Aubry, Géraldine Descamps, Patricia Gomez-Bougie, Sophie Maïga, Alban Gaignard, David Chiron, Emmanuelle Ménoret, Steven Le Gouill, Philippe Moreau, Martine Amiot, Catherine Pellat-Deceunynck
BACKGROUND: Human myeloma cell lines (HMCLs) are widely used for their representation of primary myeloma cells because they cover patient diversity, although not fully. Their genetic background is mostly undiscovered, and no comprehensive study has ever been conducted in order to reveal those details. METHODS: We performed whole-exon sequencing of 33 HMCLs, which were established over the last 50 years in 12 laboratories. Gene expression profiling and drug testing for the 33 HMCLs are also provided and correlated to exon-sequencing findings...
December 13, 2018: Journal of Hematology & Oncology
Sam A Menzies, Norbert Volkmar, Dick Jh van den Boomen, Richard T Timms, Anna S Dickson, James A Nathan, Paul J Lehner
Mammalian HMG-CoA reductase (HMGCR), the rate-limiting enzyme of the cholesterol biosynthetic pathway and the therapeutic target of statins, is post-transcriptionally regulated by sterol-accelerated degradation. Under cholesterol-replete conditions, HMGCR is ubiquitinated and degraded, but the identity of the E3 ubiquitin ligase(s) responsible for mammalian HMGCR turnover remains controversial. Using systematic, unbiased CRISPR/Cas9 genome-wide screens with a sterol-sensitive endogenous HMGCR reporter, we comprehensively map the E3 ligase landscape required for sterol-accelerated HMGCR degradation...
December 13, 2018: ELife
Nicholas J Slipek, Jyotika Varshney, David A Largaespada
Since the advent of large-scale, detailed descriptive cancer genomics studies at the beginning of the century, such as The Cancer Genome Atlas (TCGA), labs around the world have been working to make this data useful. Data like these can be made more useful by comparison with complementary functional genomic data. One new example is the application of CRISPR/Cas9-based library screening for cancer-related traits in cell lines. Such screens can reveal genome-wide suppressors of tumorigenesis and metastasis. Here we describe the use of widely available lentiviral libraries for such screens in cultured cell lines...
2019: Methods in Molecular Biology
Charles H Adelmann, Tim Wang, David M Sabatini, Eric S Lander
In this protocol, pooled sgRNA libraries targeting thousands of genes are computationally designed, generated using microarray-based synthesis techniques, and packaged into lentiviral particles. Target cells of interest are transduced with the lentiviral sgRNA pools to generate a collection of knockout mutants-via Cas9-mediated genomic cleavage-and screened for a phenotype of interest. The relative abundance of each mutant in the population can be monitored over time through high-throughput sequencing of the integrated sgRNA expression cassettes...
2019: Methods in Molecular Biology
Rebecca Kirsch, Stefan E Seemann, Walter L Ruzzo, Stephen M Cohen, Peter F Stadler, Jan Gorodkin
BACKGROUND: Comparative genomics approaches have facilitated the discovery of many novel non-coding and structured RNAs (ncRNAs). The increasing availability of related genomes now makes it possible to systematically search for compensatory base changes - and thus for conserved secondary structures - even in genomic regions that are poorly alignable in the primary sequence. The wealth of available transcriptome data can add valuable insight into expression and possible function for new ncRNA candidates...
December 11, 2018: BMC Genomics
Shi Lu, Mo Zhang, Zhuo Zhang, Zhenhui Wang, Nan Wu, Yang Song, Piwu Wang
Leaf angle and leaf orientation value are important traits affecting planting density and photosynthetic efficiency. To identify the genes involved in controlling leaf angle and leaf orientation value, we utilized 1.49×106 single nucleotide polymorphism (SNP) markers obtained after sequencing 80 backbone inbred maize lines in Jilin Province, based on phenotype data from two years, and analyzed these two traits in a genome-wide association study (GWAS). A total of 33 SNPs were significantly associated (P<0...
2018: PloS One
Chao Wang, Gang Wang, Xu Feng, Peter Shepherd, Jie Zhang, Mengfan Tang, Zhen Chen, Mrinal Srivastava, Megan E McLaughlin, Nora M Navone, Glen Traver Hart, Junjie Chen
Ataxia telangiectasia mutated and RAD3 related (ATR) protein kinase plays critical roles in ensuring DNA replication, DNA repair, and cell cycle control in response to replication stress, making ATR inhibition a promising therapeutic strategy for cancer treatment. To identify genes whose loss makes tumor cells hypersensitive to ATR inhibition, we performed CRISPR/Cas9-based whole-genome screens in 3 independent cell lines treated with a highly selective ATR inhibitor, AZD6738. These screens uncovered a comprehensive genome-wide profile of ATR inhibitor sensitivity...
December 7, 2018: Oncogene
Dan Zhou, Lei Tan, Jian Li, Tanbin Liu, Yi Hu, Yalan Li, Sachiyo Kawamoto, Chengyu Liu, Shiyin Guo, Aibing Wang
Relative to the issues of off-target effects and the difficulty of inserting a long DNA fragment in the application of designer nucleases for genome editing, embryonic stem (ES) cell-based gene-targeting technology does not have these shortcomings and is widely used to modify animal/mouse genome ranging from large deletions/insertions to single nucleotide substitutions. Notably, identifying the relatively few homologous recombination (HR) events necessary to obtain desired ES clones is a key step, which demands accurate and reliable methods...
November 20, 2018: Journal of Visualized Experiments: JoVE
Priya Hariharan, Roshan Colah, Kanjaksha Ghosh, Anita Nadkarni
The master erythroid regulator KLF1,plays a pivotal role during erythroid lineage development by regulating the expression of many erythroid genes. Variations in the KLF1 gene are found to be associated with varied erythroid phenotypes. With the aim of determining the role of KLF1 gene variations in HbF induction and their genotype phenotype relationship, in this study, we screened 370 individuals with different hemoglobinopathy condition. Hematological analysis was carried out using automated blood cell counter and Variant II HPLC (Biorad)...
December 4, 2018: Genomics
Pei Liu, Wei Wang, Jian Zhao, Dongzhi Wei
βgalactosidases have wide industrial applications in lactose hydrolysis and transglycosylation reactions. Therefore, there is a need to mine novel and high-quality β-galactosidases with good tolerance and novel features from harsh environments and genomic databases. In this study, an Escherichia coli β-galactosidase-deficient host, ΔlacZ(DE3)pRARE, was constructed by the CRISPR-Cas9 system for screening active β-galactosidases. Of thirty selected β-galactosidases, twelve novel enzymes showed β-galactosidase activity, four of which were purified for further study...
December 4, 2018: Protein Expression and Purification
Ling-Shan Yu, Jesus Rodriguez-Manzano, Kenny Malpartida-Cardenas, Thomas Sewell, Oliver Bader, Darius Armstrong-James, Matthew C Fisher, Pantelis Georgiou
Invasive human fungal infections caused by multi-azole resistant Aspergillus fumigatus are associated with increasing rates of mortality in susceptible patients. Current methods of diagnosing infections caused by multi-azole resistant A. fumigatus are, however, not well suited for use in clinical point-of-care testing or in the field. Loop-mediated isothermal amplification (LAMP) is a widely used method of nucleic acid amplification with rapid and easy-to-use features, making it suitable for use in different resource settings...
December 4, 2018: Journal of Molecular Diagnostics: JMD
Kathleen Conway, Sharon N Edmiston, Joel S Parker, Pei Fen Kuan, Yi-Hsuan Tsai, Pamela A Groben, Daniel C Zedek, Glynis A Scott, Eloise A Parrish, Honglin Hao, Michelle V Pearlstein, Jill S Frank, Craig C Carson, Matthew D Wilkerson, Xiaobei Zhao, Nathaniel A Slater, Stergios J Moschos, David W Ollila, Nancy E Thomas
Early diagnosis improves melanoma survival, yet the histopathological diagnosis of cutaneous primary melanoma can be challenging even for expert dermatopathologists. Analysis of epigenetic alterations, such as DNA methylation, that occur in melanoma can aid in its early diagnosis. Using a genome-wide methylation screen, we assessed CpG methylation in a diverse set of 89 primary invasive melanomas, 73 nevi, and 41 melanocytic proliferations of uncertain malignant potential, classified based on interobserver review by dermatopathologists...
December 6, 2018: Journal of Investigative Dermatology
Florencia Rago, Matthew T DiMare, GiNell Elliott, David A Ruddy, Sosathya Sovath, Grainne Kerr, Hyo-Eun C Bhang, Zainab Jagani
Recent studies have highlighted that cancer cells with a loss of the SWI/SNF complex catalytic subunit BRG1 are dependent on the remaining ATPase, BRM, making it an attractive target for cancer therapy. However, an understanding of the extent of target inhibition required to arrest cell growth, necessary to develop an appropriate therapeutic strategy, remains unknown. Here, we utilize tunable depletion of endogenous BRM using the SMASh degron, and interestingly observe that BRG1-mutant lung cancer cells require near complete depletion of BRM to robustly inhibit growth both in vitro and in vivo...
November 20, 2018: Biochemical and Biophysical Research Communications
Aquillah M Kanzi, Emma T Steenkamp, Nicolaas A Van der Merwe, Brenda D Wingfield
Fungi in the genus Chrysoporthe are economically important canker pathogens of commercially grown Eucalyptus species and native Myrtales. Before the current study, homothallism was widely accepted as the mating system of these species, but this hypothesis could not be fully tested. Using whole genome sequences, we characterized the MAT locus of two C. austroafricana isolates and its sibling species, C. cubensis and C. deuterocubensis. A unique MAT1-2 idiomorph containing a truncated MAT1-1-1 gene, and a MAT1-1-2 gene, was identified in one isolate of C...
December 4, 2018: Fungal Genetics and Biology: FG & B
Shouming Wu, Duoguang Wu, Yingpeng Pan, Hua Liu, Zhongfan Shao, Minghui Wang
OBJECTIVE: Recently, accumulated evidence indicates that the enhancer of zeste homologue 2 (EZH2) is highly expressed in a wide range of cancer types, including NSCLC. The downstream genes regulated by EZH2 were screened using bioinformatics analysis. This study aimed to analyse the correlation between the downstream genes of EZH2 and the prognosis of lung adenocarcinoma. METHODS: Expression and methylation data of lung adenocarcinoma were downloaded from The Cancer Genome Atlas (TCGA) (https://cancergenome...
November 24, 2018: Pathology, Research and Practice
Kristen M Cunanan, Alexia Iasonos, Ronglai Shen, Mithat Gönen
BACKGROUND: In the era of targeted therapies, clinical trials in oncology are rapidly evolving, wherein patients from multiple diseases are now enrolled and treated according to their genomic mutation(s). In such trials, known as basket trials, the different disease cohorts form the different baskets for inference. Several approaches have been proposed in the literature to efficiently use information from all baskets while simultaneously screening to find individual baskets where the drug works...
December 7, 2018: Clinical Trials: Journal of the Society for Clinical Trials
Amaranta Manrique de Lara, Liliana Soto-Gómez, Elisa Núñez-Acosta, Garbiñe Saruwatari-Zavala, Miguel E Rentería
Genome-wide association studies have revolutionized our understanding of the genetic architecture of complex traits and diseases over the last decade. This knowledge is enabling clinicians, researchers, and direct-to-consumer genetics companies to conduct disease susceptibility testing based on powerful methods such as polygenic risk scoring. However, these technologies raise a set of complex ethical, legal, social, and policy considerations. Here we review and discuss a series of ethical dilemmas associated with susceptibility genetic testing for the two most common late-onset neurodegenerative diseases, Alzheimer's and Parkinson's disease, including testing in asymptomatic individuals...
December 7, 2018: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
Jennifer Pugh, Sikandar G Khan, Deborah Tamura, Alisa M Goldstein, Maria Teresa Landi, John J DiGiovanna, Kenneth H Kraemer
Importance: Wide use of genomic sequencing to diagnose disease has raised concern about the extent of genotype-phenotype correlations. Objective: To correlate disease-associated allele frequencies with expected and reported prevalence of clinical disease. Design, Setting, and Participants: Xeroderma pigmentosum (XP), a recessive, cancer-prone, neurocutaneous disorder, was used as a model for this study. From January 1, 2017, to May 4, 2018, the Human Gene Mutation Database and a cohort of patients at the National Institutes of Health were searched and screened to identify reported mutations associated with XP...
December 5, 2018: JAMA Dermatology
Jiao Fang, Chun Gong, Yuhui Wan, Yuanyuan Xu, Fangbiao Tao, Ying Sun
BACKGROUND: Both polygenic and unhealthy lifestyle factors contribute to individual-level risk of obesity during childhood. The extent to which increased polygenic risk can be offset by healthy lifestyle is unknown. OBJECTIVE: To examine whether increased polygenic risk of obesity is modified by a healthy lifestyle during childhood. METHODS: A total of 997 children (418 boys and 579 girls) who had complete DNA genotyping and body mass index (BMI) were eligible for the study were analyzed from an established prospective puberty cohort...
December 4, 2018: Pediatric Obesity
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